Baked normal map comes out transparent
EDIT 2: FIX

Ok After some crazy amount of testing I found the culprit :D


In the render layer section, you have to check in EVERY render layer "use Surfaces".
If unchecked, you will get this strange transparent section in GPU Mode.
And in CPU mode it will even cause a crash to desktop. 

In my opinion this crash is even worth a bug report.